SNPEff eff job error

[naila2025]

Hi, I am new to galaxy and doing a practice exome sequencing data analysis. When I am using “SNPEff eff” tool the job is giving the error (please see below). I have tried multiple times but its not working. Can anyone help me please.
Thank you

Job submission failed.
The server could not complete this request. Please verify your parameter settings, retry submission and contact the Galaxy Team if this error persists. A transcript of the submitted data is shown below.
{
“history_id”: “dc4bc1e3087a51f3”,
“tool_id”: “toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff/5.2+galaxy0”,
“tool_version”: “5.2+galaxy0”,
“inputs”: {
“input”: {
“batch”: false,
“product”: false,
“values”: [
{
“id”: “4838ba20a6d86765676a2a2a7f27c9c8”,
“src”: “hda”,
“map_over_type”: null
}
]
},
“inputFormat”: “vcf”,
“outputFormat”: “vcf”,
“csvStats”: false,
“generate_stats”: true,
“snpDb|genomeSrc”: “history”,
“snpDb|snpeff_db”: {
“batch”: false,
“product”: false,
“values”: [
{
“id”: “4838ba20a6d867657379434bce0cc4cc”,
“src”: “hda”,
“map_over_type”: null
}
]
},
“snpDb|reg_section|regulation”: null,
“udLength”: “0”,
“spliceSiteSize”: “2”,
“spliceRegion|setSpliceRegions”: “no”,
“annotations”: null,
“intervals”: null,
“transcripts”: null,
“filterOut”: null,
“filter|specificEffects”: “no”,
“chr”: null,
“noLog”: true
}
}

[jennaj]

Welcome @naila2025

First, please try again. This sort of error with the pop-up should be very rare.

Then if this is still happening, we can help to determine what the problem is if you share back the history. You can also add in some screenshots if this is happening when you are submitting the job.

As an extra, I started up the workflow associated with the tutorial at UseGalaxy.org (is this where you are also working?). This should capture any technical problems on the server or with this tool specifically.

• Tutorial → Hands-on: Exome sequencing data analysis for diagnosing a genetic disease / Exome sequencing data analysis for diagnosing a genetic disease / Variant Analysis
• Workflow Invocation (with linked workflow and history both in a shared state) → https://usegalaxy.org/workflows/invocations/d9b8632ec9e7da78

How to share back is in the banner of this forum. You can post the history share link back here, then unshare once we are done.

@jennaj

How to get faster help with your question

We love details! Consider Sharing your History or posting screenshots of your Job Information Details page.

Please confirm the Server URL (your web browser at the top!) and any Tutorial links involved.

[jennaj]

Update: I think I found where the confusion might be coming from.

@naila2025

“tool_id”: “toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff/5.2+galaxy0”,
“tool_version”: “5.2+galaxy0”,

@naila2025

“generate_stats”: true,
“snpDb|genomeSrc”: “history”,
“snpDb|snpeff_db”: {

Notice how the setting was marked as using a database “from the history” but no input was selected. Also, the tutorial is using a local index from the server. Either can work but one of these needs to be supplied if the extra statistics are toggled to “yes”.

The tutorial (and workflow!) use a specific version of the snpeff tool. To gain access to the appropriate local index, use this same version when going through the steps.

• Tutorial step → Hands-on: Exome sequencing data analysis for diagnosing a genetic disease / Exome sequencing data analysis for diagnosing a genetic disease / Variant Analysis
• Version of the tool to use → SnpEff eff: annotate variants(Galaxy Version 4.3+T.galaxy2)
• How to toggle to that version → FAQ: Changing the tool version

This was just a guess – so we can follow up with your specific issue too!